The Missing Link
by Kid W25
Summary: COMPLETE. The Doctor, all by himself...finds himself in trouble. As always. But this time, there is no explanation, no idea how it started, all he knows is that he is stuck and he's got nowhere to go. Except to his family.
1. The Missing Link

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Doctor Who:

**Time Traveller**

**The Missing Link Ark**

**Episode 1:**

**The Missing Link**

The Doctor pulled down the lever and the TARDIS started. He sat down silently on the single chair inside the control room. A lot had happened in the past year. Rose had come back from the parallel universe, Martha calling him. Donna gone. He was beaten down by this. Once again he was alone.

He sighed. He stood up quickly and walked around the console in the control room.

BEEP! BEEP! BEEP! BEEP! The alarm beeped loudly.

"Oh, what now?" He stood up quickly and whizzed the computer screen around to him. Then all was silence. "Oh, no," The Doctor says.

"What's happened?" The Doctor yelled and started pressing buttons and pulling levers all around the console. Then suddenly everything stopped. "Now what?"

Everything seemed to have stopped in time except for him. Then everything seemed to go backwards. The TARDIS started to fall apart "NO! NO!" The Doctor screamed in fear.

After that everything disappeared and the Doctor was falling. And as he fell, flashes from his life from present back, went across his view in darkness.

Donna…

Martha…

Rose…

Jack Harkness…

Jenny…

The other Doctors…

His wife and kids…

His grand daughter, Susan Foreman…

With each snippet buried memories of tragedies and war bubbled up inside him. _Why is this happening?_ He cried out but no voice came. Each snippet made him weaker with sadness until after he had seen his whole life, he cried out loud-and collapse and continue to fall in the darkness.

* * *

The Doctor woke up for a start-in a hospital bed-London. He turned to his surroundings. The hospital was very busy. It was about five or six in the morning.

Through the hustle, a familiar face came along.

"Martha?" the Doctor said in surprise.

Martha checked her clipboard.."Yes, it's me , Mr.Smith. Dr.Jones .How are you feeling?"

"Aah, a bit groggy and my head's killing me but why am I on earth?" the Doctor asked.

"Probably because we're humans and we've not worked out how to live on other planets in the solar system", Martha answered cynically and started to write notes on her clipboard.

The Doctor was confused, "Wh-I know humans have not found a way to travel and live at other planets yet but they will. What I'm talking about is why am _I_ here and where is my TARDIS?"

"What's a TARDIS?" Martha asked as she wrote notes on the clipboard.

"You know-you mean…you _don't know _what I'm talking about?" the Doctor asked her.

"No, I don't know what you're talking about" Martha said.

The Doctor paused for a moment then noticed the stethoscope hanging around Martha's neck.

"Here," the Doctor said and took the stethoscope from around her head, "listen."

He placed the stethoscope onto his left heart and told Martha to listen, "see?".

"Yes, Mr. Smith, it's your heart. What's your point?" Martha asked him.

The Doctor moved the stethoscope to his right and Martha listened silently. He looked hopefully at her but all she did was sigh, wrote a few notes on her clipboard and took the stethoscope off him. "I'm sorry Mr Smith, I don't see the point. There was nothing there."

As Martha left, the Doctor slumped on his hospital bed. _I can't believe it. Was it all a dream?No! It can't be. And I'll prove it._

The Doctor was attacked by a sudden feeling of tiredness. With that he lay on his side, slid the blanket up over his shoulders and snuggled to sleep.

* * *

After sleeping for what seemed like hours, the Doctor finally woke up. There was a nurse there and when she saw him awake, "oh, he's finally awake!" and left.

The same nurse came back after with a few guests. The Doctor gasped. They were Rose and Jenny.

"Rose… Jenny?" The Doctor murmured.

Rose smiled and sobbed as she ran to the bed and hugged the Doctor. "I've missed you so much darling, the house was so dull without you." Then she kissed him.

The Doctor was surprised and pulled back.

"What's wrong?" Rose asked. The Doctor noticed the ring on her left hand and looked at his left hand and saw he had the matching ring on his left hand.

"What?" the Doctor said, looking at the ring.

"What's wrong with him Dr Jones? Doesn't he remember that he's married to me?" Rose asked Martha.

"It's only the concussion. It will go away, hopefully." Martha said.

As Rose moved away, Jenny came up and hugged the Doctor.

"He will have to stay in the hospital for a couple of days to do some tests but I'm sure that he will be alright." Martha said and smiled sweetly at Rose and Jenny.

"Thank you Dr Jones." Rose said and kissed the Doctor on the cheek, "see you soon."

* * *

Rose was crying, tears over-flowing with happiness when she saw the Doctor-John-coming out of the taxi in front of the house.

Rose and Jenny have been cleaning up the house. She remembers the small conversation that she had with Martha.

"_Mrs. Smith," Martha started._

"_Please, call me Rose," Rose interrupted._

"_Right. When he comes back home, you might need to tell him his history and try to rebuild his memory. He might fight about it and ramble about time and space and…a TARDIS. Please take a note of it and if it gets too much, call me."_

"_Yes,-can I call you Martha?" Rose asked._

"_Yes."_

Rose opened the door as John reached it.

She hugged him and Jenny did the same. John felt awkward because the last thing that he knew before the hospital bed was being in the TARDIS traveling and feeling incredibly sad and tired.

They let him through, Jenny was getting a drink for all of them as Rose led him to the sitting room and set him down next to him. "Would you like to look at some photos?" Rose asked. John felt uncomfortable. The last thing he knew was that he was on the TARDIS and that he was feeling miserable until the TARDIS had a problem. Then he remembered that he was surrounded in darkness and that he felt like he was falling.

He has no idea what was happening. Or if this is the product of one of his enemies' schemes, he has no idea how to get out of it.


	2. The Conclusion

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Episode 2:

**The Conclusion**

Years pass since the day that John woke up in the hospital. And he walked around the house and at work as if nothing is wrong. He had basically forgotten about that day and moved on. Jenny had already married and went out of the home into her own home, and Rose and John had had another baby, a baby boy this time. They decided to call him Timothy. Timothy is now 2 ½ years old and a very healthy and active boy. He is a bit taller than the average 2 ½ year old, has black hair like his father and is very advanced for his age.

When Tim was about one year old, he had said a perfect sentence. And at about 2 years old, Timothy was able to speak like 1 4 year old can. When these events happened, he had insights of his past, or what seemed to be his past. Because he is not sure what is real anymore. In his insights, he would see himself on adventures in a some sort of control room with a tower like object in the middle of the room. But as he was starting to recognise it, he would be snapped out of the sight and would never be able to remember it ever again.

John is now a writer. A writer from what Rose said was "his unlimited imagination". He created aliens, and a space/time machine named the TARDIS. His stories soon caught the eye of a publisher and his famous writing career started. And the thing about his work is that he can do anything about it. He is the publishers' top choice. And he got the top privileges because of it.

And the odd thing about his stories were, as he is writing them, he gets the feeling of familiarity. You can also call it déjà vu. But he never has a clue where the feeling came from. This always confuse him. These "déjà vu" feelings are stronger for the more recent day based stories that he wrote. Like the one where his character saves from a space ship in the shape of Titanic nearly crashed into the Buckingham Palace or the one where he had one of his main character's companions needing to leave the "TARDIS" in a very tragic way. And the fact that the companion can never remember anything about him or her brain will fry up made it the more unbearable for the readers. He got lots of awards for that story. He also felt a huge "déjà vu" feeling for that one. It seemed to him that he knew the companion and had a connection with her in real life from some point.

This had always puzzled him…

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John walked into the street one day. He needed some story ideas. As far as he knows, his stories have caught up with the present day and he has had no insights for stories ever since he's finished the latest one. He has no idea what to do. It seems that his imagination have just shut off. So that is what he's doing right now in the middle of London. Not knowing what to do. Rose is gone doing her full-time office job in a building right across London, Jenny is on a honeymoon with her husband, Keith. And Timothy is at Rose's Mum's place. Everything is perfectly normal and happy.

As John walked down the street, he felt an odd feeling that surged throughout her body. There was a woman. She walked past him and he snuck a look at her. He felt odd about it. He loved Rose so why is he looking at a total stranger for?

The woman that walked past had red hair that flowed behind her. She had a confident look on her face that made it all the more familiar. When he noticed all of this, he had a slight jolt and a single word formed in his mind…

…_Donna Noble…_

Then a flood of memories flowed into his brain that made him double over, clutching his head. He fell, elbows on the ground and stayed there for a second or two when he felt a hand on his left shoulder pulling him around. Donna's face filled his view.

"What the hell is wrong with you? You made me trip over your leg." She stood up and walked off. John heard her say, "seriously. Men these days." And to that comment he thought one sentence in his mind that made him have another jolt. The sentence was: _typical Donna_.

He moaned painfully. It felt like something was trying to force the thoughts about Donna out of his head. He rolled around on the footpath and the people passing just stared at him and walked off. As he opened his eyes, he saw a few people taking videos from their mobile phones. _This probably will go on YouTube, _he thought. He fought the godly force to take out his thoughts on Donna and could see a shape fading into nothing in the distance. He gasped. Not only because of the jab that he felt in his stomach, but it was also the TARDIS.

The TARDIS was the object that was fading out into nothing.

* * *

He woke up again and found himself in a hospital. A familiar face looked at his once more. It was Dr. Jones'. "Welcome back Mr. Smith." She said in a flat voice. "What do you have now? You know you should stop getting yourself into a hospital or you would be seeing my unfriendly face every time you wake up" she continued in a more light, happy voice.

"What happened?" John said, his voice sounded a bit croaky.

"Apparently, you fell unconscious in the street and have been in a –" she looked at her notebook, she looked surprised, "surprisingly short coma. You've only been in it for an hour or two. Amazing"

She wrote notes on her clipboard. "So, do you know have any ideas why you collapsed in the middle of the streets and wake up out of a coma a couple of hours later?"

He just shook his head. He had absolutely no idea.

She just nodded and said as she walked off. "There's someone here to see you." And then he found himself in the embrace of a crying Rose.

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A few months later, John had managed to publish his latest book, claiming that it will be the last one for a while, claiming that he needed to take a break. The latest story was about a being that had somehow managed to get into the TARDIS and got 'The Doctor', his main character, in a some sort of dream. Leaving 'The Doctor' helpless. But in this dream world, he managed to remember who he was, what he was, where he was and most importantly, when he was. It became an instant bestseller, like all of his other stories.

Feeling finally at peace, John walked down the same street that he collapsed a few months ago. He thought, if I had a story idea from here, maybe I could get one once more. The thing is, for him now, writing 'The Doctor' stories have become an addictive thing. Even though he said to the press that he needs a rest, he just itches for more.

He walked and stood still at the spot that he collapsed at and as he looked at his surroundings, he saw a familiar figure walking off into the distance. He decided to follow this man but his legs wouldn't allow him. It was the same force that he felt months ago that tried to force the thoughts about Donna in his mind. He gasped. _Donna!_

As John fought the force, he managed to step forward. That seemed to lift the force's power a bit. Soon after, he managed another step, and then another. Soon he was able to shake off the power and ran after the familiar figure.

He caught up with the man and spun him around. He looked at him and stuttered. "Y-you're…"

He nodded and said one word. "You."

* * *

The Doctor and John walked up to the TARDIS. The Doctor looked at John and gave him a small key. "Go ahead," the Doctor said. John slowly grabbed the keys from the Doctor's hands and stepped forward. He placed the keys into the keyhole and slowly turned the key around until he heard a click. Then, he reached at the door handle of the police box and pulled it open.

He was flooded by white light and everything seemed to disappear around him and then he found himself in the TARDIS floor. He groggily stood up and looked around. He suddenly knew what had happened. It was just like his latest story. It was a foreign alien being that had sneaked on to the TARDIS probably as he was going into the TARDIS last time. When he dropped Donna to her own house. The being probably chased after him all this time and managed to finally catch up.

The alien being seemed to have disappeared. The Doctor didn't know if the alien being had died because he went out of the dream world or fled seeing how strong the Doctor was. The Doctor smiled.

_Strong. Strong? _The Doctor thought as he pulled and pushed a few levers and watched quietly as the TARDIS started making its trademark noise and whirred to who knows where.

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_**Author's Note:**__ I'm sorry for people who might have read the first chapter, but I'm sorry if this ending is not strong enough to be your liking. And if there are any mistakes (which I'm sure there will be) please ignore them. Thanks._

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Jackasniceguy

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